Testbed
Basic formatting
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
italic text
bold text
strike-through text
Text with extra blank lines above and below
- list item a
- list item b
- list item c
- ordered list item 1
- ordered list item 2
- ordered list item 3
- top level list item
- nested list item
- even deeper nested list item
- nested list item
Plain image:
Heading 1
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
Heading 2
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
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Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
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Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
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| TABLE | Game 1 | Game 2 | Game 3 | Total |
|---|---|---|---|---|
| Anna | 144 | 123 | 218 | 485 |
| Bill | 90 | 175 | 120 | 385 |
| Cara | 102 | 214 | 233 | 549 |
It was the best of times it was the worst of times. It was the age of wisdom, it was the age of foolishness. It was the spring of hope, it was the winter of despair.
// some code with syntax highlighting
const popup = document.querySelector("#popup");
popup.style.width = "100%";
popup.innerText =
"Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.";
This sentence has inline code, useful for making references to variables, packages, versions, etc. within a sentence.
Lorem ipsum dolor sit amet.
Consectetur adipiscing elit.
Sed do eiusmod tempor incididunt.
Hidden content
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
Jekyll Spaceship
| Stage | Direct Products | ATP Yields |
|---|---|---|
| Glycolysis
|
2 ATP | |
| 2 NADH | 3–5 ATP | |
| Pyruvaye oxidation | 2 NADH | 5 ATP |
| Citric acid cycle
|
2 ATP | |
| 6 NADH | 15 ATP | |
| 2 FADH | 3 ATP | |
| 30–32 ATP |
$ a * b = c ^ b $
$ 2^{\frac{n-1}{3}} $
$ \int_a^b f(x)\,dx. $
Components
Section
Section, background
Section, dark=true
Section, background dark=true
Section, size=wide
Section, size=full w/ figure
Figure
px width
% width
px height
px width, svg
% width, svg
px height, svg
Button
Icon
Lorem Ipsum Dolor
Feature
Title
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
Title
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
List
List citations
2025
Yield Determination in Major Small Grain Crops in Response to Nitrogen Fertilization
Plants
·
24 Mar 2025
·
doi:10.3390/plants14071017
Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data
Bioinformatics
·
22 Mar 2025
·
doi:10.1093/bioinformatics/btaf122
Biological databases in the age of generative artificial intelligence.
Bioinformatics advances
·
20 Mar 2025
·
pmid:40177265
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs.
Molecular systems biology
·
01 Feb 2025
·
pmid:39762653
2024
Simplicity within biological complexity
Bioinformatics Advances
·
26 Dec 2024
·
doi:10.1093/bioadv/vbae164
Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks
Bioinformatics
·
01 Nov 2024
·
doi:10.1093/bioinformatics/btae650
MONFIT: multi-omics factorization-based integration of time-series data sheds light on Parkinson’s disease
NAR Molecular Medicine
·
24 Sep 2024
·
doi:10.1093/narmme/ugae012
Current and future directions in network biology
Bioinformatics advances
·
14 Aug 2024
·
pmc:PMC11321866
Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing
Nucleic acids research
·
05 Jul 2024
·
pmc:PMC11223884
MONFIT: Multi-omics factorization-based integration of time-series data sheds light on Parkinson’s disease
openRxiv
·
03 Jun 2024
·
doi:10.1101/2024.06.03.597147
The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell
Bioinformatics advances
·
23 May 2024
·
pmc:PMC11142626
Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson's disease.
Scientific reports
·
14 May 2024
·
pmid:38744869
2023
Genetic progress in grain yield and associated changes in spikelet and grain traits in historical set of Pannonian wheat cultivars
Euphytica
·
16 Dec 2023
·
doi:10.1007/s10681-023-03262-6
Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson’s disease
openRxiv
·
13 Dec 2023
·
doi:10.1101/2023.12.12.570554
Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks
openRxiv
·
01 Nov 2023
·
doi:10.1101/2023.10.27.564419
The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell
openRxiv
·
02 Aug 2023
·
doi:10.1101/2023.07.31.551263
A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma.
Cancer gene therapy
·
07 Jul 2023
·
pmid:37420093
Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing
ArXiv
·
04 Jul 2023
·
pmc:PMC10274948
A phenotype driven integrative framework uncovers molecular mechanisms of a rare hereditary thrombophilia.
PloS one
·
25 Apr 2023
·
pmid:37098010
A functional analysis of omic network embedding spaces reveals key altered functions in cancer
Bioinformatics
·
21 Apr 2023
·
doi:10.1093/bioinformatics/btad281
Integrated Data Analysis Uncovers New COVID-19 Related Genes and Potential Drug Re-Purposing Candidates
International Journal of Molecular Sciences
·
11 Jan 2023
·
doi:10.3390/ijms24021431
2022
Identifying cellular cancer mechanisms through pathway-driven data integration
Bioinformatics (Oxford, England)
·
15 Sep 2022
·
pmc:PMC9477533
Big Data to Knowledge Analytics Reveals the Zika Virus Epidemic as Only One of Multiple Factors Contributing to a Year-Over-Year 28-Fold Increase in Microcephaly Incidence
International journal of environmental research and public health
·
25 Jul 2022
·
pmc:PMC9331749
Graphlet eigencentralities capture novel central roles of genes in pathways.
PloS one
·
25 Jan 2022
·
pmid:35077468
2021
Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets.
Bioinformatics (Oxford, England)
·
11 Dec 2021
·
pmid:34375392
Linear functional organization of the omic embedding space
Bioinformatics (Oxford, England)
·
05 Nov 2021
·
pmc:PMC8570782
Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates.
Scientific reports
·
23 Sep 2021
·
pmid:34556735
Classification in biological networks with hypergraphlet kernels.
Bioinformatics (Oxford, England)
·
17 May 2021
·
pmid:32886115
Between viral targets and differentially expressed genes in COVID-19: the sweet spot for therapeutic intervention.
Springer Science and Business Media LLC
·
28 Jan 2021
·
doi:10.21203/rs.3.rs-152622/v2
Between viral targets and differentially expressed genes in COVID-19: the sweet spot for therapeutic intervention.
Springer Science and Business Media LLC
·
22 Jan 2021
·
doi:10.21203/rs.3.rs-152622/v1
2020
Probabilistic graphlets capture biological function in probabilistic molecular networks.
Bioinformatics (Oxford, England)
·
30 Dec 2020
·
pmid:33381834
Chromatin network markers of leukemia.
Bioinformatics (Oxford, England)
·
01 Jul 2020
·
pmid:32657405
Unveiling new disease, pathway, and gene associations via multi-scale neural network.
PloS one
·
06 Apr 2020
·
pmid:32251458
2019
Graphlet Laplacians for topology-function and topology-disease relationships.
Bioinformatics (Oxford, England)
·
15 Dec 2019
·
pmid:31192358
Antiproliferative activity and mode of action analysis of novel amino and amido substituted phenantrene and naphtho[2,1-b]thiophene derivatives.
European journal of medicinal chemistry
·
06 Nov 2019
·
pmid:31734024
Functional geometry of protein interactomes.
Bioinformatics (Oxford, England)
·
01 Oct 2019
·
pmid:30821317
Author Correction: Towards a data-integrated cell.
Nature communications
·
21 May 2019
·
pmid:31113941
Analyzing Network Data in Biology and Medicine
Cambridge University Press
·
18 Mar 2019
·
doi:10.1017/9781108377706
Towards a data-integrated cell
Nature communications
·
18 Feb 2019
·
pmc:PMC6379402
Analyzing network data in biology and medicine: an interdisciplinary textbook for biological, medical and computational scientists
Cambridge University Press
·
01 Jan 2019
·
isbn:978-1-108-42175-1
Analyzing network data in biology and medicine: an interdisciplinary textbook for biological, medical and computational scientists
Cambridge university press
·
01 Jan 2019
·
isbn:9781108432238
2018
Critical Review on Zeolite Clinoptilolite Safety and Medical Applications
Frontiers in pharmacology
·
27 Nov 2018
·
pmid:30538633
Higher-order molecular organization as a source of biological function.
Bioinformatics (Oxford, England)
·
01 Sep 2018
·
pmid:30423061
Precision medicine ― A promising, yet challenging road lies ahead
Current Opinion in Systems Biology
·
01 Feb 2018
·
doi:10.1016/j.coisb.2017.10.003
2017
Omics Data Complementarity Underlines Functional Cross-Communication in Yeast.
Journal of integrative bioinformatics
·
10 Jun 2017
·
pmid:28600905
Unified Alignment of Protein-Protein Interaction Networks.
Scientific reports
·
19 Apr 2017
·
pmid:28424527
Rebuttal to the Letter to the Editor in response to the paper: proper evaluation of alignment-free network comparison methods.
Bioinformatics (Oxford, England)
·
01 Apr 2017
·
pmid:28073757
Systematic protein-protein interaction mapping for clinically relevant human GPCRs.
Molecular systems biology
·
15 Mar 2017
·
pmid:28298427
2016
Graphlet-based Characterization of Directed Networks.
Scientific reports
·
13 Oct 2016
·
pmid:27734973
A global genetic interaction network maps a wiring diagram of cellular function.
Science (New York, N.Y.)
·
23 Sep 2016
·
pmid:27708008
NETWORK ANALYSIS. Network analytics in the age of big data.
Science (New York, N.Y.)
·
08 Jul 2016
·
pmid:27387938
Integrative methods for analyzing big data in precision medicine.
Proteomics
·
01 Mar 2016
·
pmid:26677817
PATIENT-SPECIFIC DATA FUSION FOR CANCER STRATIFICATION AND PERSONALISED TREATMENT.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
·
01 Jan 2016
·
pmid:26776197
Computational Methods for Integration of Biological Data
Europeanization and Globalization
·
01 Jan 2016
·
doi:10.1007/978-3-319-39349-0_8
2015
Fuse: multiple network alignment via data fusion.
Bioinformatics (Oxford, England)
·
14 Dec 2015
·
pmid:26668003
Methods for biological data integration: perspectives and challenges.
Journal of the Royal Society, Interface
·
06 Nov 2015
·
pmid:26490630
Proper evaluation of alignment-free network comparison methods.
Bioinformatics (Oxford, England)
·
24 Mar 2015
·
pmid:25810431
L-GRAAL: Lagrangian graphlet-based network aligner.
Bioinformatics (Oxford, England)
·
28 Feb 2015
·
pmid:25725498
Topology-function conservation in protein-protein interaction networks.
Bioinformatics (Oxford, England)
·
20 Jan 2015
·
pmid:25609797
ergm.graphlets: A Package for ERG Modeling Based on Graphlet Statistics
Journal of Statistical Software
·
01 Jan 2015
·
doi:10.18637/jss.v065.i12
2014
The integrated disease network.
Integrative biology : quantitative biosciences from nano to macro
·
01 Nov 2014
·
pmid:25133803
Network wiring of pleiotropic kinases yields insight into protective role of diabetes on aneurysm.
Integrative biology : quantitative biosciences from nano to macro
·
01 Nov 2014
·
pmid:25098752
Anti-nicastrin monoclonal antibodies elicit pleiotropic anti-tumour pharmacological effects in invasive breast cancer cells.
Breast cancer research and treatment
·
24 Sep 2014
·
pmid:25248409
Predicting disease associations via biological network analysis.
BMC bioinformatics
·
17 Sep 2014
·
pmid:25228247
Integration of molecular network data reconstructs Gene Ontology.
Bioinformatics (Oxford, England)
·
01 Sep 2014
·
pmid:25161252
The topology of the growing human interactome data.
Journal of integrative bioinformatics
·
23 Jun 2014
·
pmid:24953453
Bridging the gaps in systems biology.
Molecular genetics and genomics : MGG
·
13 Apr 2014
·
pmid:24728588
Revealing the hidden language of complex networks.
Scientific reports
·
01 Apr 2014
·
pmid:24686408
Survey of network-based approaches to research of cardiovascular diseases.
BioMed research international
·
20 Mar 2014
·
pmid:24772427
Modelling the yeast interactome.
Scientific reports
·
04 Mar 2014
·
pmid:24589662
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity.
Bioinformatics (Oxford, England)
·
17 Jan 2014
·
pmid:24443377
Erratum to: Anti-nicastrin monoclonal antibodies elicit pleiotropic anti-tumour pharmacological effects in invasive breast cancer cells
Breast Cancer Research and Treatment
·
01 Jan 2014
·
pmc:PMC4643546
2013
The role of genes co-amplified with nicastrin in breast invasive carcinoma.
Breast cancer research and treatment
·
13 Dec 2013
·
pmid:24337538
Discovering disease-disease associations by fusing systems-level molecular data.
Scientific reports
·
15 Nov 2013
·
pmid:24232732
Network topology reveals key cardiovascular disease genes.
PloS one
·
15 Aug 2013
·
pmid:23977067
Graphlet-based measures are suitable for biological network comparison.
Bioinformatics (Oxford, England)
·
23 Jan 2013
·
pmid:23349212
2012
The Core Diseasome.
Molecular bioSystems
·
01 Oct 2012
·
pmid:22820726
Biological function through network topology: a survey of the human diseasome.
Briefings in functional genomics
·
08 Sep 2012
·
pmid:22962330
C-GRAAL: common-neighbors-based global GRAph ALignment of biological networks.
Integrative biology : quantitative biosciences from nano to macro
·
10 Jan 2012
·
pmid:22234340
Functional coherence of molecular networks in bioinformatics
Springer
·
01 Jan 2012
·
isbn:9781461403203
Bacterial molecular networks: methods and protocols
Humana Press
·
01 Jan 2012
·
isbn:9781617793608
Protein complex prediction with RNSC.
Methods in molecular biology (Clifton, N.J.)
·
01 Jan 2012
·
pmid:22144160
2011
A framework for FPGA acceleration of large graph problems: Graphlet counting case study
2011 International Conference on Field-Programmable Technology
·
01 Dec 2011
·
doi:10.1109/FPT.2011.6132667
Introduction to the Special Issue on Biological Networks
Internet Mathematics
·
28 Nov 2011
·
doi:10.1080/15427951.2011.621769
Random Graph Models and Their Application to Protein–Protein Interaction Networks
Handbook of Statistical Systems Biology
·
12 Sep 2011
·
doi:10.1002/9781119970606.ch14
Dominating biological networks.
PloS one
·
26 Aug 2011
·
pmid:21887225
Topological Characteristics of Molecular Networks
Functional Coherence of Molecular Networks in Bioinformatics
·
24 Aug 2011
·
doi:10.1007/978-1-4614-0320-3_2
Evidence for network evolution in an Arabidopsis interactome map.
Science (New York, N.Y.)
·
29 Jul 2011
·
pmid:21798944
Integrative network alignment reveals large regions of global network similarity in yeast and human.
Bioinformatics (Oxford, England)
·
16 Mar 2011
·
pmid:21414992
Protein-protein interactions: making sense of networks via graph-theoretic modeling.
BioEssays : news and reviews in molecular, cellular and developmental biology
·
01 Feb 2011
·
pmid:21188720
GraphCrunch 2: Software tool for network modeling, alignment and clustering.
BMC bioinformatics
·
19 Jan 2011
·
pmid:21244715
Bioinformatics For Biologists
Cambridge University Press
·
01 Jan 2011
·
isbn:9781139501613
2010
Optimal network alignment with graphlet degree vectors.
Cancer informatics
·
30 Jun 2010
·
pmid:20628593
Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets.
BMC systems biology
·
15 Jun 2010
·
pmid:20550706
Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy.
Journal of proteome research
·
05 Apr 2010
·
pmid:20170199
Complementarity of network and sequence information in homologous proteins.
Journal of integrative bioinformatics
·
25 Mar 2010
·
pmid:20375452
An integrative approach to modeling biological networks.
Journal of integrative bioinformatics
·
25 Mar 2010
·
pmid:20375453
Topological network alignment uncovers biological function and phylogeny.
Journal of the Royal Society, Interface
·
17 Mar 2010
·
pmid:20236959
Biological network comparison using graphlet degree distribution
Bioinformatics
·
03 Mar 2010
·
doi:10.1093/bioinformatics/btq091
Geometric evolutionary dynamics of protein interaction networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
·
01 Jan 2010
·
pmid:19908370
From Topology to Phenotype in Protein–Protein Interaction Networks
Network Science
·
01 Jan 2010
·
doi:10.1007/978-1-84996-396-1_3
Biological data mining
Chapman & Hall/CRC
·
01 Jan 2010
·
isbn:978-1-4200-8684-3
2009
Geometric de-noising of protein-protein interaction networks.
PLoS computational biology
·
07 Aug 2009
·
pmid:19662157
Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data.
Journal of the Royal Society, Interface
·
22 Jul 2009
·
pmid:19625303
Optimized null model for protein structure networks.
PloS one
·
26 Jun 2009
·
pmid:19557139
Structure of brain functional networks.
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
·
01 Jan 2009
·
pmid:19964621
Learning the structure of protein-protein interaction networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
·
01 Jan 2009
·
pmid:19209694
2008
Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis.
Proceedings of the National Academy of Sciences of the United States of America
·
29 Aug 2008
·
pmid:18757749
Uncovering biological network function via graphlet degree signatures.
Cancer informatics
·
14 Apr 2008
·
pmid:19259413
Fitting a geometric graph to a protein-protein interaction network.
Bioinformatics (Oxford, England)
·
14 Mar 2008
·
pmid:18344248
GraphCrunch: a tool for large network analyses.
BMC bioinformatics
·
30 Jan 2008
·
pmid:18230190
2007
Geometric Local Structure in Biological Networks
2007 IEEE Information Theory Workshop
·
01 Sep 2007
·
doi:10.1109/ITW.2007.4313108
Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution.
PLoS computational biology
·
01 Jul 2007
·
pmid:17616981
Biological network comparison using graphlet degree distribution.
Bioinformatics (Oxford, England)
·
15 Jan 2007
·
pmid:17237089
2006
Modelling protein-protein interaction networks via a stickiness index.
Journal of the Royal Society, Interface
·
22 Oct 2006
·
pmid:16971339
Efficient estimation of graphlet frequency distributions in protein-protein interaction networks.
Bioinformatics (Oxford, England)
·
01 Feb 2006
·
pmid:16452112
2005
2-Tree probe interval graphs have a large obstruction set
Discrete Applied Mathematics
·
01 Sep 2005
·
doi:10.1016/j.dam.2004.06.015
High-throughput mapping of a dynamic signaling network in mammalian cells.
Science (New York, N.Y.)
·
11 Mar 2005
·
pmid:15761153
2004
Modeling interactome: scale-free or geometric?
Bioinformatics (Oxford, England)
·
29 Jul 2004
·
pmid:15284103
Protein complex prediction via cost-based clustering.
Bioinformatics (Oxford, England)
·
04 Jun 2004
·
pmid:15180928
Functional topology in a network of protein interactions.
Bioinformatics (Oxford, England)
·
12 Feb 2004
·
pmid:14960460
Hereditary dominating pair graphs
Discrete Applied Mathematics
·
01 Jan 2004
·
doi:10.1016/S0166-218X(03)00304-4
1998
Minimum Average Time Broadcast Graphs
Parallel Processing Letters
·
01 Jun 1998
·
doi:10.1142/s012962649800016x
ISSN 1535-9476 - Molecular & cellular proteomics (Print)
·
·
issn:1535-9476
Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation
Lecture Notes in Computer Science
·
·
doi:10.1007/978-3-540-73060-6_1
ISSN 1176-9351 - Cancer informatics.
·
·
issn:1176-9351
ISSN 1742-464X - The FEBS journal (Print)
·
·
issn:1742-464X
List projects
List team members
<div class="portrait-wrapper"> <a
href="/members/aleksandr-matsun.html"
class="portrait"
data-style=""
aria-label="Aleksandr Matsun" >
<i class="icon">
<span class="fi fi-ru"></span>
</i>
<img
src="/images/team/aleksandr-matsun.jpeg"
class="portrait-image"
alt="Aleksandr Matsun"
loading="lazy"
onerror="this.src='/images/fallback.svg'; this.onerror=null;"
>
<span class="portrait-name">Aleksandr Matsun</span>
<span class="portrait-description">
Research Engineer
</span>
</a> </div>
<div class="portrait-wrapper"> <a
href="/members/branislava-jankovic.html"
class="portrait"
data-style=""
aria-label="Branislava Jankovic" >
<i class="icon">
<span class="fi fi-rs"></span>
</i>
<img
src="/images/team/branislava-jankovic.jpeg"
class="portrait-image"
alt="Branislava Jankovic"
loading="lazy"
onerror="this.src='/images/fallback.svg'; this.onerror=null;"
>
<span class="portrait-name">Branislava Jankovic</span>
<span class="portrait-description">
PhD Student
</span>
</a> </div>
<div class="portrait-wrapper"> <a
href="/members/natasa-przulj.html"
class="portrait"
data-style=""
aria-label="Natasa Przulj" >
<i class="icon">
<span class="fi fi-gb"></span>
</i>
<img
src="/images/team/natasa-przulj.jpeg"
class="portrait-image"
alt="Natasa Przulj"
loading="lazy"
onerror="this.src='/images/fallback.svg'; this.onerror=null;"
>
<span class="portrait-name">Natasa Przulj</span>
<span class="portrait-description">
Principal Investigator
</span>
</a> </div>
<div class="portrait-wrapper"> <a
href="/members/noel-malod.html"
class="portrait"
data-style=""
aria-label="Noel Malod-Dognin" >
<i class="icon">
<span class="fi fi-fr"></span>
</i>
<img
src="/images/team/noel-malod.jpeg"
class="portrait-image"
alt="Noel Malod-Dognin"
loading="lazy"
onerror="this.src='/images/fallback.svg'; this.onerror=null;"
>
<span class="portrait-name">Noel Malod-Dognin</span>
<span class="portrait-description">
Research Scientist
</span>
</a> </div>
<div class="portrait-wrapper"> <a
href="/members/sam-windels.html"
class="portrait"
data-style=""
aria-label="Sam F. L. Windels" >
<i class="icon">
<span class="fi fi-be"></span>
</i>
<img
src="/images/team/sam-windels.jpeg"
class="portrait-image"
alt="Sam F. L. Windels"
loading="lazy"
onerror="this.src='/images/fallback.svg'; this.onerror=null;"
>
<span class="portrait-name">Sam F. L. Windels</span>
<span class="portrait-description">
Postdoctoral Associate
</span>
</a> </div>
<div class="portrait-wrapper"> <a
href="/members/stevan-milinkovic.html"
class="portrait"
data-style=""
aria-label="Stevan Milinkovic" >
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<span class="portrait-name">Stevan Milinkovic</span>
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Research Scientist
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<span class="portrait-name">Tarmo Nurmi</span>
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Postdoctoral Associate
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2025
Yield Determination in Major Small Grain Crops in Response to Nitrogen Fertilization
Plants
·
24 Mar 2025
·
doi:10.3390/plants14071017
Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data
Bioinformatics
·
22 Mar 2025
·
doi:10.1093/bioinformatics/btaf122
Biological databases in the age of generative artificial intelligence.
Bioinformatics advances
·
20 Mar 2025
·
pmid:40177265
Author Correction: Systematic protein-protein interaction mapping for clinically relevant human GPCRs.
Molecular systems biology
·
01 Feb 2025
·
pmid:39762653
2024
Simplicity within biological complexity
Bioinformatics Advances
·
26 Dec 2024
·
doi:10.1093/bioadv/vbae164
Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks
Bioinformatics
·
01 Nov 2024
·
doi:10.1093/bioinformatics/btae650
MONFIT: multi-omics factorization-based integration of time-series data sheds light on Parkinson’s disease
NAR Molecular Medicine
·
24 Sep 2024
·
doi:10.1093/narmme/ugae012
Current and future directions in network biology
Bioinformatics advances
·
14 Aug 2024
·
pmc:PMC11321866
Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing
Nucleic acids research
·
05 Jul 2024
·
pmc:PMC11223884
MONFIT: Multi-omics factorization-based integration of time-series data sheds light on Parkinson’s disease
openRxiv
·
03 Jun 2024
·
doi:10.1101/2024.06.03.597147
The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell
Bioinformatics advances
·
23 May 2024
·
pmc:PMC11142626
Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson's disease.
Scientific reports
·
14 May 2024
·
pmid:38744869
2023
Genetic progress in grain yield and associated changes in spikelet and grain traits in historical set of Pannonian wheat cultivars
Euphytica
·
16 Dec 2023
·
doi:10.1007/s10681-023-03262-6
Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson’s disease
openRxiv
·
13 Dec 2023
·
doi:10.1101/2023.12.12.570554
Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks
openRxiv
·
01 Nov 2023
·
doi:10.1101/2023.10.27.564419
The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell
openRxiv
·
02 Aug 2023
·
doi:10.1101/2023.07.31.551263
A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma.
Cancer gene therapy
·
07 Jul 2023
·
pmid:37420093
Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing
ArXiv
·
04 Jul 2023
·
pmc:PMC10274948
A phenotype driven integrative framework uncovers molecular mechanisms of a rare hereditary thrombophilia.
PloS one
·
25 Apr 2023
·
pmid:37098010
A functional analysis of omic network embedding spaces reveals key altered functions in cancer
Bioinformatics
·
21 Apr 2023
·
doi:10.1093/bioinformatics/btad281
Integrated Data Analysis Uncovers New COVID-19 Related Genes and Potential Drug Re-Purposing Candidates
International Journal of Molecular Sciences
·
11 Jan 2023
·
doi:10.3390/ijms24021431
2022
Identifying cellular cancer mechanisms through pathway-driven data integration
Bioinformatics (Oxford, England)
·
15 Sep 2022
·
pmc:PMC9477533
Big Data to Knowledge Analytics Reveals the Zika Virus Epidemic as Only One of Multiple Factors Contributing to a Year-Over-Year 28-Fold Increase in Microcephaly Incidence
International journal of environmental research and public health
·
25 Jul 2022
·
pmc:PMC9331749
Graphlet eigencentralities capture novel central roles of genes in pathways.
PloS one
·
25 Jan 2022
·
pmid:35077468
2021
Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets.
Bioinformatics (Oxford, England)
·
11 Dec 2021
·
pmid:34375392
Linear functional organization of the omic embedding space
Bioinformatics (Oxford, England)
·
05 Nov 2021
·
pmc:PMC8570782
Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates.
Scientific reports
·
23 Sep 2021
·
pmid:34556735
Classification in biological networks with hypergraphlet kernels.
Bioinformatics (Oxford, England)
·
17 May 2021
·
pmid:32886115
Between viral targets and differentially expressed genes in COVID-19: the sweet spot for therapeutic intervention.
Springer Science and Business Media LLC
·
28 Jan 2021
·
doi:10.21203/rs.3.rs-152622/v2
Between viral targets and differentially expressed genes in COVID-19: the sweet spot for therapeutic intervention.
Springer Science and Business Media LLC
·
22 Jan 2021
·
doi:10.21203/rs.3.rs-152622/v1
2020
Probabilistic graphlets capture biological function in probabilistic molecular networks.
Bioinformatics (Oxford, England)
·
30 Dec 2020
·
pmid:33381834
Chromatin network markers of leukemia.
Bioinformatics (Oxford, England)
·
01 Jul 2020
·
pmid:32657405
Unveiling new disease, pathway, and gene associations via multi-scale neural network.
PloS one
·
06 Apr 2020
·
pmid:32251458
2019
Graphlet Laplacians for topology-function and topology-disease relationships.
Bioinformatics (Oxford, England)
·
15 Dec 2019
·
pmid:31192358
Antiproliferative activity and mode of action analysis of novel amino and amido substituted phenantrene and naphtho[2,1-b]thiophene derivatives.
European journal of medicinal chemistry
·
06 Nov 2019
·
pmid:31734024
Functional geometry of protein interactomes.
Bioinformatics (Oxford, England)
·
01 Oct 2019
·
pmid:30821317
Author Correction: Towards a data-integrated cell.
Nature communications
·
21 May 2019
·
pmid:31113941
Analyzing Network Data in Biology and Medicine
Cambridge University Press
·
18 Mar 2019
·
doi:10.1017/9781108377706
Towards a data-integrated cell
Nature communications
·
18 Feb 2019
·
pmc:PMC6379402
Analyzing network data in biology and medicine: an interdisciplinary textbook for biological, medical and computational scientists
Cambridge University Press
·
01 Jan 2019
·
isbn:978-1-108-42175-1
Analyzing network data in biology and medicine: an interdisciplinary textbook for biological, medical and computational scientists
Cambridge university press
·
01 Jan 2019
·
isbn:9781108432238
2018
Critical Review on Zeolite Clinoptilolite Safety and Medical Applications
Frontiers in pharmacology
·
27 Nov 2018
·
pmid:30538633
Higher-order molecular organization as a source of biological function.
Bioinformatics (Oxford, England)
·
01 Sep 2018
·
pmid:30423061
Precision medicine ― A promising, yet challenging road lies ahead
Current Opinion in Systems Biology
·
01 Feb 2018
·
doi:10.1016/j.coisb.2017.10.003
2017
Omics Data Complementarity Underlines Functional Cross-Communication in Yeast.
Journal of integrative bioinformatics
·
10 Jun 2017
·
pmid:28600905
Unified Alignment of Protein-Protein Interaction Networks.
Scientific reports
·
19 Apr 2017
·
pmid:28424527
Rebuttal to the Letter to the Editor in response to the paper: proper evaluation of alignment-free network comparison methods.
Bioinformatics (Oxford, England)
·
01 Apr 2017
·
pmid:28073757
Systematic protein-protein interaction mapping for clinically relevant human GPCRs.
Molecular systems biology
·
15 Mar 2017
·
pmid:28298427
2016
Graphlet-based Characterization of Directed Networks.
Scientific reports
·
13 Oct 2016
·
pmid:27734973
A global genetic interaction network maps a wiring diagram of cellular function.
Science (New York, N.Y.)
·
23 Sep 2016
·
pmid:27708008
NETWORK ANALYSIS. Network analytics in the age of big data.
Science (New York, N.Y.)
·
08 Jul 2016
·
pmid:27387938
Integrative methods for analyzing big data in precision medicine.
Proteomics
·
01 Mar 2016
·
pmid:26677817
PATIENT-SPECIFIC DATA FUSION FOR CANCER STRATIFICATION AND PERSONALISED TREATMENT.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
·
01 Jan 2016
·
pmid:26776197
Computational Methods for Integration of Biological Data
Europeanization and Globalization
·
01 Jan 2016
·
doi:10.1007/978-3-319-39349-0_8
2015
Fuse: multiple network alignment via data fusion.
Bioinformatics (Oxford, England)
·
14 Dec 2015
·
pmid:26668003
Methods for biological data integration: perspectives and challenges.
Journal of the Royal Society, Interface
·
06 Nov 2015
·
pmid:26490630
Proper evaluation of alignment-free network comparison methods.
Bioinformatics (Oxford, England)
·
24 Mar 2015
·
pmid:25810431
L-GRAAL: Lagrangian graphlet-based network aligner.
Bioinformatics (Oxford, England)
·
28 Feb 2015
·
pmid:25725498
Topology-function conservation in protein-protein interaction networks.
Bioinformatics (Oxford, England)
·
20 Jan 2015
·
pmid:25609797
ergm.graphlets: A Package for ERG Modeling Based on Graphlet Statistics
Journal of Statistical Software
·
01 Jan 2015
·
doi:10.18637/jss.v065.i12
2014
The integrated disease network.
Integrative biology : quantitative biosciences from nano to macro
·
01 Nov 2014
·
pmid:25133803
Network wiring of pleiotropic kinases yields insight into protective role of diabetes on aneurysm.
Integrative biology : quantitative biosciences from nano to macro
·
01 Nov 2014
·
pmid:25098752
Anti-nicastrin monoclonal antibodies elicit pleiotropic anti-tumour pharmacological effects in invasive breast cancer cells.
Breast cancer research and treatment
·
24 Sep 2014
·
pmid:25248409
Predicting disease associations via biological network analysis.
BMC bioinformatics
·
17 Sep 2014
·
pmid:25228247
Integration of molecular network data reconstructs Gene Ontology.
Bioinformatics (Oxford, England)
·
01 Sep 2014
·
pmid:25161252
The topology of the growing human interactome data.
Journal of integrative bioinformatics
·
23 Jun 2014
·
pmid:24953453
Bridging the gaps in systems biology.
Molecular genetics and genomics : MGG
·
13 Apr 2014
·
pmid:24728588
Revealing the hidden language of complex networks.
Scientific reports
·
01 Apr 2014
·
pmid:24686408
Survey of network-based approaches to research of cardiovascular diseases.
BioMed research international
·
20 Mar 2014
·
pmid:24772427
Modelling the yeast interactome.
Scientific reports
·
04 Mar 2014
·
pmid:24589662
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity.
Bioinformatics (Oxford, England)
·
17 Jan 2014
·
pmid:24443377
Erratum to: Anti-nicastrin monoclonal antibodies elicit pleiotropic anti-tumour pharmacological effects in invasive breast cancer cells
Breast Cancer Research and Treatment
·
01 Jan 2014
·
pmc:PMC4643546
2013
The role of genes co-amplified with nicastrin in breast invasive carcinoma.
Breast cancer research and treatment
·
13 Dec 2013
·
pmid:24337538
Discovering disease-disease associations by fusing systems-level molecular data.
Scientific reports
·
15 Nov 2013
·
pmid:24232732
Network topology reveals key cardiovascular disease genes.
PloS one
·
15 Aug 2013
·
pmid:23977067
Graphlet-based measures are suitable for biological network comparison.
Bioinformatics (Oxford, England)
·
23 Jan 2013
·
pmid:23349212
2012
The Core Diseasome.
Molecular bioSystems
·
01 Oct 2012
·
pmid:22820726
Biological function through network topology: a survey of the human diseasome.
Briefings in functional genomics
·
08 Sep 2012
·
pmid:22962330
C-GRAAL: common-neighbors-based global GRAph ALignment of biological networks.
Integrative biology : quantitative biosciences from nano to macro
·
10 Jan 2012
·
pmid:22234340
Functional coherence of molecular networks in bioinformatics
Springer
·
01 Jan 2012
·
isbn:9781461403203
Bacterial molecular networks: methods and protocols
Humana Press
·
01 Jan 2012
·
isbn:9781617793608
Protein complex prediction with RNSC.
Methods in molecular biology (Clifton, N.J.)
·
01 Jan 2012
·
pmid:22144160
2011
A framework for FPGA acceleration of large graph problems: Graphlet counting case study
2011 International Conference on Field-Programmable Technology
·
01 Dec 2011
·
doi:10.1109/FPT.2011.6132667
Introduction to the Special Issue on Biological Networks
Internet Mathematics
·
28 Nov 2011
·
doi:10.1080/15427951.2011.621769
Random Graph Models and Their Application to Protein–Protein Interaction Networks
Handbook of Statistical Systems Biology
·
12 Sep 2011
·
doi:10.1002/9781119970606.ch14
Dominating biological networks.
PloS one
·
26 Aug 2011
·
pmid:21887225
Topological Characteristics of Molecular Networks
Functional Coherence of Molecular Networks in Bioinformatics
·
24 Aug 2011
·
doi:10.1007/978-1-4614-0320-3_2
Evidence for network evolution in an Arabidopsis interactome map.
Science (New York, N.Y.)
·
29 Jul 2011
·
pmid:21798944
Integrative network alignment reveals large regions of global network similarity in yeast and human.
Bioinformatics (Oxford, England)
·
16 Mar 2011
·
pmid:21414992
Protein-protein interactions: making sense of networks via graph-theoretic modeling.
BioEssays : news and reviews in molecular, cellular and developmental biology
·
01 Feb 2011
·
pmid:21188720
GraphCrunch 2: Software tool for network modeling, alignment and clustering.
BMC bioinformatics
·
19 Jan 2011
·
pmid:21244715
Bioinformatics For Biologists
Cambridge University Press
·
01 Jan 2011
·
isbn:9781139501613
2010
Optimal network alignment with graphlet degree vectors.
Cancer informatics
·
30 Jun 2010
·
pmid:20628593
Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets.
BMC systems biology
·
15 Jun 2010
·
pmid:20550706
Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy.
Journal of proteome research
·
05 Apr 2010
·
pmid:20170199
Complementarity of network and sequence information in homologous proteins.
Journal of integrative bioinformatics
·
25 Mar 2010
·
pmid:20375452
An integrative approach to modeling biological networks.
Journal of integrative bioinformatics
·
25 Mar 2010
·
pmid:20375453
Topological network alignment uncovers biological function and phylogeny.
Journal of the Royal Society, Interface
·
17 Mar 2010
·
pmid:20236959
Biological network comparison using graphlet degree distribution
Bioinformatics
·
03 Mar 2010
·
doi:10.1093/bioinformatics/btq091
Geometric evolutionary dynamics of protein interaction networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
·
01 Jan 2010
·
pmid:19908370
From Topology to Phenotype in Protein–Protein Interaction Networks
Network Science
·
01 Jan 2010
·
doi:10.1007/978-1-84996-396-1_3
Biological data mining
Chapman & Hall/CRC
·
01 Jan 2010
·
isbn:978-1-4200-8684-3
2009
Geometric de-noising of protein-protein interaction networks.
PLoS computational biology
·
07 Aug 2009
·
pmid:19662157
Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data.
Journal of the Royal Society, Interface
·
22 Jul 2009
·
pmid:19625303
Optimized null model for protein structure networks.
PloS one
·
26 Jun 2009
·
pmid:19557139
Structure of brain functional networks.
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
·
01 Jan 2009
·
pmid:19964621
Learning the structure of protein-protein interaction networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
·
01 Jan 2009
·
pmid:19209694
2008
Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis.
Proceedings of the National Academy of Sciences of the United States of America
·
29 Aug 2008
·
pmid:18757749
Uncovering biological network function via graphlet degree signatures.
Cancer informatics
·
14 Apr 2008
·
pmid:19259413
Fitting a geometric graph to a protein-protein interaction network.
Bioinformatics (Oxford, England)
·
14 Mar 2008
·
pmid:18344248
GraphCrunch: a tool for large network analyses.
BMC bioinformatics
·
30 Jan 2008
·
pmid:18230190
2007
Geometric Local Structure in Biological Networks
2007 IEEE Information Theory Workshop
·
01 Sep 2007
·
doi:10.1109/ITW.2007.4313108
Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution.
PLoS computational biology
·
01 Jul 2007
·
pmid:17616981
Biological network comparison using graphlet degree distribution.
Bioinformatics (Oxford, England)
·
15 Jan 2007
·
pmid:17237089
2006
Modelling protein-protein interaction networks via a stickiness index.
Journal of the Royal Society, Interface
·
22 Oct 2006
·
pmid:16971339
Efficient estimation of graphlet frequency distributions in protein-protein interaction networks.
Bioinformatics (Oxford, England)
·
01 Feb 2006
·
pmid:16452112
2005
2-Tree probe interval graphs have a large obstruction set
Discrete Applied Mathematics
·
01 Sep 2005
·
doi:10.1016/j.dam.2004.06.015
High-throughput mapping of a dynamic signaling network in mammalian cells.
Science (New York, N.Y.)
·
11 Mar 2005
·
pmid:15761153
2004
Modeling interactome: scale-free or geometric?
Bioinformatics (Oxford, England)
·
29 Jul 2004
·
pmid:15284103
Protein complex prediction via cost-based clustering.
Bioinformatics (Oxford, England)
·
04 Jun 2004
·
pmid:15180928
Functional topology in a network of protein interactions.
Bioinformatics (Oxford, England)
·
12 Feb 2004
·
pmid:14960460
Hereditary dominating pair graphs
Discrete Applied Mathematics
·
01 Jan 2004
·
doi:10.1016/S0166-218X(03)00304-4
1998
Minimum Average Time Broadcast Graphs
Parallel Processing Letters
·
01 Jun 1998
·
doi:10.1142/s012962649800016x
ISSN 1535-9476 - Molecular & cellular proteomics (Print)
·
·
issn:1535-9476
Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation
Lecture Notes in Computer Science
·
·
doi:10.1007/978-3-540-73060-6_1
ISSN 1176-9351 - Cancer informatics.
·
·
issn:1176-9351
ISSN 1742-464X - The FEBS journal (Print)
·
·
issn:1742-464X
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